I have (h)MeDip data from two different cell types I would like to compare to identify D(h)MR between the two cells. I used MACS 2 to call peaks and calculated a enrichment value according to this formula:
which is more or less the log2 fold ration of sequencing reads for a peak between antibody treated sample and non-antibody treated control (normalized by total number of reads). To compare now my two cells I calculated the log2fold change of the mean of the enrichment value (I have all experiments in triplicates) of the two cell types. Using this strategy I identify several regions with great GO terms of the nearest gene (which makes absolutely sense in the biological context of the experiment).
However I calculate a log2fold change with numbers already on a log2fold scale, sounds a bit weird for me (however iam a biologist and have no clue about mathematics in general ;) ). Furthermore i tried simply to calculate the fold change and setting up new cutoff parameters comparable to the previous used on the log2 scale, however i loss a lot of potential DMR regions.
Therefor can i continue to calculate the log2fold ration of the two enrichment values or is this simply wrong ? Alternatives ?
Thanks a lot,